ABC managing director Mark Scott is standing by the broadcaster's reporting of asylum seeker allegations against the Navy and resisting calls to apologise.

The ABC has come under fire from Prime Minister Tony Abbott and several of his senior ministers over its reporting of claims by asylum seekers that they were mistreated by Navy personnel during a tow-back to Indonesian waters.

ABC News aired video footage of asylum seekers receiving medical assessments of burns that Indonesian police say were inflicted by the Australian Navy.

Mr Abbott says he is very disappointed with the ABC's story, which he said contained uncorroborated reports of alleged mistreatment, and has led calls for the broadcaster to apologise to the Navy.

Federal Labor frontbencher Jason Clare today joined those calls, saying that the ABC once apologised for putting "false" allegations to him during an interview.

"I was able to prove it with evidence that the information they provided was wrong and they apologised. It was the right thing to do then and it's the right thing to do now," he told Sky News.

However, speaking to ABC Local Radio in Melbourne this morning, Mr Scott defended the way the story was handled.

"I think there are some suggestions here that those allegations should not have been reported, there's some suggestion here that that video tape should not have been aired," he said.

"We stand by that, we stand by the thrust of the story, and I think it is important that we be judged on that story.

"One of the reasons we've pursued this story is that we do greatly respect and admire the Australian Navy.

"I've pointed out to people the top-rating show on ABC television last year was the review of the Australian Navy.

"It's our role as journalists to ask those questions and that's what our news team has been doing, and I back them in doing it."

When asked this morning if he would "offer up a scalp" over the organisation's handling of the issue, he replied "no" and declared that he is standing firmly in the role and has not considered resigning.

He revealed that he had spoken to previous ABC general managers and delved into the broadcaster's history, and concluded that from time to time there were stories people disagreed with and which caused upset.

However, this was par for the course in all media organisations, he said.